On Thu, Jan 3, 2019 at 3:10 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

The first command does not work because --slabel requires three options
and it is interpreting "--i" and "/Volumes...mgh" as those two so it
thinks you have not included. It is probably better to use something like
mri_segstats --seg ocn.mgh --excludeid 0 --avgwf test.dat
--sumTest_SupParietal.sum --i lh.thickness.fwhm10.fsaverage.mgh

On 1/3/19 2:41 PM, Tamara Sussman wrote:
>
>         External Email - Use Caution
>
> Thanks so much for your suggestion, Douglas.
> Here is the whole input and output:
>
> Tamara-Posner-lab:~ posnerlab$ mri_segstats --slabel
> /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
> --i/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
> --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
>
> ERROR: cannot do frame average without input volume
>
>
> I was using --slabel instead of --seg because I am using surfaces, and
> not volumes. Just to test it out, I tried using the --seg aseg too,
> and got the same error:
>
> Tamara-Posner-lab:~ posnerlab$ mri_segstats --seg
> /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/mri/aseg.mgz
> --mask
> /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
> --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
>
> ERROR: cannot do frame average without input volume
>
> Thank you again for your help!
> Tamara
>
>
> On Thu, Jan 3, 2019 at 1:59 PM Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>
> Can you include the full command line (no $variables) and the full
> terminal output?
>
> On 1/2/19 4:22 PM, Tamara Sussman wrote:
> >
> >         External Email - Use Caution
> >
> > Thanks for your response - yes, I should have included this
> > information before. :)
> >
> > $label was set to a label I made by 1. binarizing the cluster
> results
> > from the previous analysis, and then 2. using mri_vol2label to
> convert
> > this into a label
> >
> >
> label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
> >
> >
> > $input was set to an individual's thickness data (analogous data
> that
> > I used in the initial analysis):
> >
> input=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
> >
> > On Wed, Jan 2, 2019 at 4:09 PM <ts+ml@rcmd.org
> <mailto:ts%2Bml@rcmd.org>
> > <mailto:ts%2Bml@rcmd.org <mailto:ts%252Bml@rcmd.org>>> wrote:
> >
> >    External Email - Use Caution
> >
> > What are $label and $input set to?
> >
> > > On January 2, 2019 at 9:13 PM Tamara Sussman
> <tsussman@gmail.com <mailto:tsussman@gmail.com>
> > <mailto:tsussman@gmail.com <mailto:tsussman@gmail.com>>> wrote:
> > >
> > >
> > > External Email - Use Caution
> > >
> > > Hello Freesurfer Experts!
> > >
> > > Thank you in advance for considering this question.
> > >
> > > I did a cortical thickness analysis (surface-based), and
> found a
> > > significant cluster. I found the average cortical
> thickness in*
> > this group*,
> > > in the .*y.ocn.dat* file, which is great.
> > >
> > > Now I want to find the average cortical thickness in the same
> > cluster, in a
> > > separate group of subjects.
> > >
> > > I tried using mri_segstats, but it doesn't seem to work:
> > >
> > > mri_segstats --slabel $label --i $input --nonempty --excludeid
> > 0 --avgwf
> > > test.dat --sum Test_SupParietal.sum
> > >
> > > The error I am getting is:
> > >
> > > ERROR: cannot do frame average without input volume
> > >
> > > Any thoughts about a better way to approach this analysis?
> > >
> > > Thanks again in advance!
> > > -T
> > > _______________________________________________
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> >
> > --
> > Dr. Tim Schäfer
> > Postdoc Computational Neuroimaging
> > Department of Child and Adolescent Psychiatry,
> Psychosomatics and
> > Psychotherapy
> > University Hospital Frankfurt, Goethe University Frankfurt am
> > Main, Germany
> >
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